\(^1\) GenomEast platform, IGBMC
- Log in to Galaxy

Once done, please visit this page.
- History
- Create a new
history

- Change the name of
the history to “DNA-seq data analysis”
- Change the name of the new history to “DNA-seq data analysis” by
clicking on the pencil next to the history name. Then, click on “Unnamed
history” on top of the history panel, enter “DNA-seq data analysis” and
click save.

- Importing files from
your computer to Galaxy
- Download the file “sample.bed.gz” following this link and
upload it to Galaxy.
- The genome is: Mouse (mm9)
- The format is: bed
You should be in the history “DNA-seq data analysis” (Switch to it if
needed)
- Download the file “sample.bed.gz” and upload it into Galaxy in the
history called “DNA-seq data analysis”
- Click on “Upload Data”
- Drag and drop the file sample.bed to the window that popped up.
- The genome is : Mouse (mm9)
- The format is : bed

- Remove a dataset
- Remove the dataset sample.bed.gz from your history
by clicking on the button

- You are told that your history is empty. Look at the size of your
history
- Click on “Show deleted” in the top of the history
panel. Remove definitely the file from the disk by clicking on
“Purge All Deleted Content”.
- Click on “Show active”

- Create a workflow out
of an existing history
One can create a workflow from an existing history going to the
history button and selecting “Extract Workflow”.
- Rename the workflow
“DNA-seq data analysis”

- Edit a workflow with
the workflow editor
- Open the workflow
editor with the workflow “DNA-seq data analysis”
- Click on Workflow (top menu)
- Click on DNA-seq data analysis in the list of
workflows
- Select edit

An interactive view of the workflow is displayed: 
You can move the boxes to make the workflow clearer: 
- Add steps to the
workflow
Your workflow should look like this before editing:

Add the following tools:
- Samtools flagstat to compute mapping statistics
(after BWA mem)
- Filter SAM or BAM, output SAM or BAM to select
aligned reads with a mapping quality >= 20 (after
MarkDuplicates)
- Samtools flagstat to compute mapping statistics
after removing reads with low mapping qualities (after Filter)
Here are the parameters to use for each of the tools:
- Flagstat tabulate descriptive stats for BAM dataset
- BAM File to Convert: output of BWA mem
- Filter SAM or BAM, output SAM or BAM files on FLAG
MAPQ RG LN or by region
- SAM or BAM file to filter: output of Picard
MarkDuplicates
- Minimum MAPQ quality score: 20
- Flagstat tabulate descriptive stats for BAM dataset
- BAM File to Convert: output of Filter
The final workflow should look like this (new tools are in purple
boxes):
